MolNFT v1 · #21673 · protein

Ephrin A5 ligand structure

1SHX · Ephrin-A5: “Ephrin A5 ligand structure”. X-ray diffraction, 1 ligand (NAG), 2 pockets (best druggability 0.39). MolNFT v1 #21673 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1SHX
Type: protein
Length: 276 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ephrin-A5
UniProt: O08543
Ligands: NAG
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ephrin-A5	protein	138	7% helix, 34% strand	O08543

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	92	0.39	0.77	18	empty
2	84	0.35	0.75	20	empty

Modifications

Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

1SHX · Ephrin A5 ligand structure · the same entry in another collection · chain A against A, TM-score 1.00
O08543 · AlphaFold monomer V2.0 prediction for ephrin-A5 (O08543) · a predicted model of the same protein · chain B against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O08543
Elsewhere: RCSB PDB 1SHX · PDBe 1SHX · UniProt O08543

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